# run_fceri_gamma2.bngl
# load and run FCERI model (gamma2 variant) using NF, HPP and SSA methods
version("2.2.4+")
setModelName("fceri_gamma2")
readFile({file=>"fceri_gamma2.bngl",allow_actions=>0})

# configure HPP
begin parameters
    # fraction of cell to simulate
    f  0.001
    # population lumping rate, /s
    k_lump 10000
end parameters
begin population maps
    # HPP1 only lumps free ligand
    Lig(l,l) -> X0001()  k_lump
    # HPP6 also lumps the following
    Lyn(U,SH2) -> X0002()  k_lump
    Syk(tSH2,l~Y,a~Y) -> X0003()  k_lump
    Syk(tSH2,l~Y,a~pY) -> X0004()  k_lump
    Syk(tSH2,l~pY,a~Y) -> X0005()  k_lump
    Syk(tSH2,l~pY,a~pY) -> X0006()  k_lump
end population maps

# actions:
saveConcentrations()
# simulate with NFsim #prefix=>"fceri_gamma2", 
simulate_nf({ suffix=>"nf", t_end=>1200, n_steps=>120, gml=>10000000, complex=>1, get_final_state=>0 })
# generate partial network and simulate with HPP
resetConcentrations()
generate_hybrid_model({ suffix=>"hpp", overwrite=>1, verbose=>1, execute=>1,\
                        actions=>["simulate_nf({ t_end=>1200, n_steps=>120 ,gml=>10000000, complex=>0 })"] })
# generate reaction network and simulate with SSA 
resetConcentrations()
generate_network({ overwrite=>1, max_iter=>2 })
simulate_ssa({ suffix=>"ssa", t_end=>1200,n_steps=>120, print_CDAT=>0 })